[BioSQL-l] Re: Ontology names

[David Block]

The obvious ones should be enumerated as well:
Sequence Ontology
Relationship Ontology (coming soon)
Molecular Function
Cellular Component
Biological Process

any more?

On Friday, September 27, 2002, at 11:52  AM, Hilmar Lapp wrote:

> As may have been anticipated (at least I did), ontology_term is going 
> to be used quite heavily and in important places. Essentially we're 
> going to use several ontologies, and they'll all be in ontology_term. 
> The way to constrain a term to a certain ontology is by its FK to 
> itself (category_id), which should point to the name of the ontology 
> the term belongs to. There is a UK on (term_name,category_id).
>
> Ontology names will likely (but are not required to) have NULL in 
> category_id.
>
> Is everyone OK with this so far?
>
> In order to get things out by a Bio* package other than the one that 
> put it in, we need to agree on ontology names in the first place (but 
> also on terms).
>
> I am right now using the following ontology names:
>
> - 'Annotation Tags': the keys (tags, qualifier names) for simple 
> annotation values (qualifier values)
> - 'SeqFeature Keys': the keys of seqfeatures ($feat->primary_tag() slot 
> in bioperl; e.g., the genbank feature key, or swissprot feature key, 
> like 'CDS', 'mRNA', ...)
> - 'SeqFeature Sources': the source names of seqfeatures 
> ($feat->source_tag() slot in bioperl; like 'swissprot', 'genscan', etc).
>
> There is already a pre-defined number of terms for location properties 
> (min_start, etc), but without an ontology. I'd like to put them into an 
> ontology and suggest the name 'Location Tags' for it.
>
> Any ideas, comments, etc. more than welcome.
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
--
David Block                                  dblock@gnf.org
GNF - San Diego, CA             http://www.gnf.org
Genome Informatics / Enterprise Programming
Weblog:      http://radio.weblogs.com/0104507/